tbuckley/cabot-search huggingface dataset:
Origin and Evolution of Marsupial-specific Imprinting Clusters Through Lineage-specific Gene Duplications and Acquisition of Promoter Differential Methylation
Authors: Wenqi Cao, Kory C Douglas, Paul B Samollow, John L VandeBerg, Xu Wang, Andrew G Clark
Journal: Molecular Biology and Evolution (2023)

Abstract Genomic imprinting is a parent-of-origin-specific expression phenomenon that plays fundamental roles in many biological processes. In animals, imprinting is only observed in therian mammals, with ∼200 imprinted genes known in humans and mice. The imprinting pattern in marsupials has been minimally investigated by examining orthologs to known eutherian imprinted genes. To identify marsupial-specific imprinting in an unbiased way, we performed RNA-seq studies on samples of fetal brain and placenta from the reciprocal cross progeny of two laboratory opossum stocks. We inferred allele-specific expression for &amp;gt;3,000 expressed genes and discovered/validated 13 imprinted genes, including three previously known imprinted genes, Igf2r, Peg10, and H19. We estimate that marsupials imprint ∼60 autosomal genes, which is a much smaller set compared with eutherians. Among the nine novel imprinted genes, three noncoding RNAs have no known homologs in eutherian mammals, while the remaining genes have important functions in pluripotency, transcription regulation, nucleolar homeostasis, and neural differentiation. Methylation analyses at promoter CpG islands revealed differentially methylated regions in five of these marsupial-specific imprinted genes, suggesting that differential methylation is a common mechanism in the epigenetic regulation of marsupial imprinting. Clustering and co-regulation were observed at marsupial imprinting loci Pou5f3-Npdc1 and Nkrfl-Ipncr2, but eutherian-type multi-gene imprinting clusters were not detected. Also differing from eutherian mammals, the brain and placenta imprinting profiles are remarkably similar in opossums, presumably due to the shared origin of these organs from the trophectoderm. Our results contribute to a fuller understanding of the origin, evolution, and mechanisms of genomic imprinting in therian mammals.
18F-FDG PET/CT and 68Ga-DOTA-FAPI-04 PET/CT Findings of Myeloid Sarcoma
Authors: Wei Liu, Xiao Yang, Liming Chen, Yue Chen, Tingting Xu
Journal: Clinical Nuclear Medicine (2022)

A 28-year-old woman presented with a 2-month history of swelling and pain in the chest wall. An irregular soft tissue mass in the chest wall and mediastinum was showed on chest CT. 18F-FDG PET/CT revealed obvious FDG uptake in the mass. Subsequently, the patient was participated in a 68Ga-DOTA-FAPI-04 PET/CT tumor clinical trial. 68Ga-DOTA-FAPI-04 PET/CT also showed elevated tracer uptake in the mass. Biopsy of the mass confirmed a diagnosis of myeloid sarcoma.
The pollutome-connectome axis: a putative mechanism to explain pollution effects on neurodegeneration
Authors: Lorenzo Pini, Alessandro Salvalaggio, Alexandra M. Wennberg, Anastasia Dimakou, Michela Matteoli, Maurizio Corbetta
Journal: Ageing Research Reviews (2023)

The study of pollutant effects is extremely important to address the epochal challenges we are facing, where world populations are increasingly moving from rural to urban centers, revolutionizing our world into an urban world. These transformations will exacerbate pollution, thus highlighting the necessity to unravel its effect on human health. Epidemiological studies have reported that pollution increases the risk of neurological diseases, with growing evidence on the risk of neurodegenerative disorders. Air pollution and water pollutants are the main chemicals driving this risk. These chemicals can promote inflammation, acting in synergy with genotype vulnerability. However, the biological underpinnings of this association are unknown. In this review, we focus on the link between pollution and brain network connectivity at the macro-scale level. We provide an updated overview of epidemiological findings and studies investigating brain network changes associated with pollution exposure, and discuss the mechanistic insights of pollution-induced brain changes through neural networks. We explain, in detail, the pollutome-connectome axis that might provide the functional substrate for pollution-induced processes leading to cognitive impairment and neurodegeneration. We describe this model within the framework of two pollutants, air pollution, a widely recognized threat, and polyfluoroalkyl substances, a large class of synthetic chemicals which are currently emerging as new neurotoxic source.
The American Psychiatric Association Practice Guideline for the Treatment of Patients With Eating Disorders
Authors: Catherine Crone, Laura J. Fochtmann, Evelyn Attia, Robert Boland, Javier Escobar, Victor Fornari, Neville Golden, Angela Guarda, Maga Jackson-Triche, Laurie Manzo, Margherita Mascolo, Karen Pierce, Megan Riddle, Andreea Seritan, Blair Uniacke, Nancy Zucker, Joel Yager, Thomas J. Craig, Seung-Hee Hong, Jennifer Medicus
Journal: American Journal of Psychiatry (2023)
Atypically Intense Pharmacologically Induced Brown Fat Activation on FDG PET/CT
Authors: Pavan Brahmbhatt, Fatemeh Ataei, Ephraim E. Parent, Akash Sharma
Journal: Clinical Nuclear Medicine (2023)

Brown fat activation with increased radiotracer localization on FDG PET/CT studies is a well-known phenomenon. Activated brown adipose tissue (BAT) is usually seen in the supraclavicular region, but also in paraspinal and rarely in upper abdominal fat. Ours is a unique case of atypically intense, multilobular FDG uptake in activated BAT. Chart review revealed that the patient was receiving mirabegron, a known activator of brown fat. Methods of reducing brown fat uptake are known, but little information is reported on pharmacologic causes of increased uptake. Factors increasing FDG uptake in BAT should also be considered when interpreting PET/CT studies.
Obsessive-Compulsive Disorder and Its Cross-Generational Familial Association With Anxiety Disorders in a National Swedish Extended Adoption Study
Authors: Kenneth S. Kendler, Linda Abrahamsson, Henrik Ohlsson, Jan Sundquist, Kristina Sundquist
Journal: JAMA Psychiatry (2023)

We know little about the transmission of obsessive-compulsive disorder (OCD) across generations.
Detection of Malpositioned VP Shunt Catheter by Radionuclide CSF Cisternography
Authors: Nahyun Jo, Gautam Edhayan, Shahin Owji, Javier Villanueva-Meyer, Peeyush Bhargava
Journal: Clinical Nuclear Medicine (2023)

Abstract A 37-year-old man presented with a 2-week history of abdominal pain, headaches, nausea, vomiting, and leukocytosis. Medical history includes congenital hydrocephalus, with a ventriculoperitoneal shunt placed several years ago. Radionuclide cerebrospinal fluid cisternography shows curvilinear activity in the abdomen, in the pattern of small and large bowel loops, suggesting that the tip of the catheter is inside a small bowel loop. No activity is seen in the intraperitoneal compartment. CT of the abdomen and pelvis followed by laparoscopic surgery confirmed the findings.
Vasopressors or High-Volume IV Fluids Both Effective for Sepsis
Authors: Howard Larkin
Journal: JAMA (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Gastric Mucosal Viability Assessment Using 99mTcO4 in a Case of Pure Esophageal Atresia After Isoperistaltic Gastric Tube Replacement
Authors: Sneha Prakash, Rakesh Kumar, Madhavi Tripathi, Vimalendu Jha, Minu Bajpai
Journal: Clinical Nuclear Medicine (2022)

Abstract Gastric surface mucosal cells are responsible for the uptake and secretion of 99m TcO 4 , a feature that has been used in imaging heterotopic gastric mucosa. We used the same principle to look for gastric mucosal viability in this case of pure esophageal atresia admitted for cervical stomal closure after a previous isoperistaltic gastric tube (IGT) replacement procedure. 99m TcO 4 scintigraphy was done after encountering a failure to maneuver the esophagoscope through the IGT. The study was helpful in assessing the loss of gastric mucosal viability in an intervening segment of the IGT.
National Academies: Expand US Wastewater Disease Surveillance
Authors: Howard Larkin
Journal: JAMA (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
68Ga-FAPI PET/CT Imaging of Intracranial Syphilitic Gumma
Authors: Weidong Gong, Shuang Qiu, Shiyu Zheng, Wei Liu, Chunyin Zhang
Journal: Clinical Nuclear Medicine (2022)

Abstract Intracranial syphilitic gumma is a rare neurological disease. We present 68 Ga-DOTA-FAPI-04 and 18 F-FDG PET/CT findings of intracranial syphilitic gumma in a 46-year-old man with HIV. In this case, 68 Ga-DOTA-FAPI-04 PET/CT outperforms 18 F-FDG in helping to visualizing syphilitic gumma. Syphilitic gumma can also cause increase FAPI activity. Our findings suggest the potential value of 68 Ga-DOTA-FAPI-04 in the diagnosis of syphilis.
Clinicopathologic and Molecular Subtyping of EGFR Mutation—Letter
Authors: Steven Sorscher
Journal: Clinical Cancer Research (2023)

Jung and colleagues found that among patients with EGFR-mutated non–small cell lung cancer (NSCLC), patients with tumor molecular profiles that also demonstrated a TP53 mutation had “poor recurrence-free survival (RFS) independent of pStage II or IIIA” and concluded that a novel adjuvant treatment strategy “needs to be investigated” for these patients. Thus, their report suggests that the dual biomarker EGFR/TP53 mutation is a predictor of poor RFS (1).There are two groups of patients with tumors showing the dual biomarker EGFR/TP53 mutations. The authors did not discuss how the RFS of those with the dual biomarker EGFR/TP53 mutations compared between patients who were confirmed to have Li Fraumeni syndrome (LFS) and patients who did not have LFS.Roughly 15% of NSCLCs have EGFR mutations and Labbe reported that dual TP53/EGFR mutations were found in 43 of 105 (41%) patients (2). Skoulidis and Heymach reviewed the results from several studies and estimated that dual TP53/EGFR mutations occur in 60% of NSCLCs (3).Patients with LFS and NSCLC, typically have EGFR-mutated NSCLC, including one study showing that 26 of 30 patients with LFS had EGFR-mutated NSCLC (4, 5). Benusiglio and colleagues concluded “for unknown reasons, the majority of Li Fraumeni-associated lung adenocarcinomas harbor EGFR somatic activating variants.” Regarding referral to genetics clinics for LFS exploration they suggested, “In our opinion, too little prominence is given to lung adenocarcinoma.” (4).Because 2%–7% of NSCLCs are thought to be LFS related, if germline testing (GT) is recommended for these 7.5% of patients with NSCLC, it can be estimated that half will be confirmed to have LFS (4).Jung and colleagues nicely showed that dual TP53/EGFR mutations predicted poor RFS. GT should be considered in patients with this dual biomarker to diagnose those patients with LFS, as there are recommended measures to diagnose early LFS-associated cancers in those patients and affected family members. Future reports might compare the RFS between those with dual TP53/EGFR mutations and LFS and the RFS among those with dual EGFR/TP53 mutations who do not have LFS to establish whether LFS is a more or less accurate predictor of RFS among patients whose tumors demonstrate the dual biomarker EGFR/TP53 mutations.See the Response, p. 687S. Sorscher reports other support from Invitae, Corp outside the submitted work. No other disclosures were reported.
Association of Resident Independence With Short-term Clinical Outcome in Core General Surgery Procedures
Authors: Celsa M. Tonelli, Tyler Cohn, Zaid Abdelsattar, Frederick A. Luchette, Marshall S. Baker
Journal: JAMA Surgery (2023)

Importance Prior studies evaluating the effect of resident independence on operative outcome draw from case mixes that cross disciplines and overrepresent cases with low complexity. The association between resident independence and clinical outcome in core general surgical procedures is not well defined. Objective To evaluate the level of autonomy provided to residents during their training, trends in resident independence over time, and the association between resident independence in the operating room and clinical outcome. Design, Setting, and Participants Using the Veterans Affairs Surgical Quality Improvement Program database from 2005 to 2021, outcomes in resident autonomy were compared using multivariable logistic regression and propensity score matching. Data on patients undergoing appendectomy, cholecystectomy, partial colectomy, inguinal hernia, and small-bowel resection in a procedure with a resident physician involved were included. Exposures Resident independence was graded as the attending surgeon scrubbed into the operation (AS) or the attending surgeon did not scrub (ANS). Main Outcomes and Measures Outcomes of interest included rates of postoperative complication, severity of complications, and death. Results Of 109 707 patients who met inclusion criteria, 11 181 (10%) underwent operations completed with ANS (mean [SD] age of patients, 61 [14] years; 10 527 [94%] male) and 98 526 (90%) operations completed with AS (mean [SD] age of patients, 63 [13] years; 93 081 [94%] male). Appendectomy (1112 [17%]), cholecystectomy (3185 [11%]), and inguinal hernia (5412 [13%]) were more often performed with ANS than small-bowel resection (527 [6%]) and colectomy (945 [4%]). On multivariable logistic regression adjusting for procedure type, age, body mass index, functional status, comorbidities, American Society of Anesthesiologists class, wound class, case priority, admission status, facility type, and year, factors associated with a complication included increasing age (adjusted odds ratio [aOR], 1.19 [95% CI, 1.16-1.22]), emergent case priority (aOR, 1.41 [95% CI, 1.33-1.50]), and resident independence (aOR, 1.12 [95% CI, 1.03-1.22]). On propensity score matching, AS cases were score matched 1:1 to ANS cases based on the variables listed above. Comparing matched cohorts, there was no difference in complication rates (817 [7%] vs 784 [7%]) or death (91 [1%] vs 102 [1%]) based on attending physician involvement. Conclusions and Relevance Core general surgery cases performed by senior-level trainees in such a way that the attending physician is not scrubbed into the case are being done safely with no significant difference in rates of postoperative complication.
Moving toward Equitable Care for Sleep Apnea in the United States: Positive Airway Pressure Adherence Thresholds: An Official American Thoracic Society Policy Statement
Authors: Anna M. May, Sanjay R. Patel, Motoo Yamauchi, Tilak K. Verma, Terri E. Weaver, Ching Li Chai-Coetzer, J. Daryl Thornton, Gary Ewart, Terrance Showers, Najib T. Ayas, Sairam Parthasarathy, Reena Mehra, Martha E. Billings
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

Section:ChooseTop of pageAbstract <<IntroductionBackgroundMethodsRecommendationsDiscussionReferences
Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells
Authors: Francesco Maura, Bachisio Ziccheddu, Jenny Z. Xiang, Bhavneet Bhinder, Joel Rosiene, Federico Abascal, Kylee H. Maclachlan, Kenneth Wha Eng, Manik Uppal, Feng He, Wei Zhang, Qi Gao, Venkata D. Yellapantula, Vicenta Trujillo-Alonso, Sunita I. Park, Matthew J. Oberley, Elizabeth Ruckdeschel, Megan S. Lim, Gerald B. Wertheim, Matthew J. Barth, Terzah M. Horton, Andriy Derkach, Alexandra E. Kovach, Christopher J. Forlenza, Yanming Zhang, Ola Landgren, Craig H. Moskowitz, Ethel Cesarman, Marcin Imielinski, Olivier Elemento, Mikhail Roshal, Lisa Giulino-Roth
Journal: Blood Cancer Discovery (2023)

The rarity of malignant Hodgkin and Reed Sternberg (HRS) cells in classic Hodgkin lymphoma (cHL) limits the ability to study the genomics of cHL. To circumvent this, our group has previously optimized fluorescence-activated cell sorting to purify HRS cells. Using this approach, we now report the whole-genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events leading to cHL. We identified alterations in driver genes not previously described in cHL, APOBEC mutational activity, and the presence of complex structural variants including chromothripsis. We found that high ploidy in cHL is often acquired through multiple, independent chromosomal gains events including whole-genome duplication. Evolutionary timing analyses revealed that structural variants enriched for RAG motifs, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID-driven mutagenesis usually preceded large chromosomal gains. This study provides a temporal reconstruction of cHL pathogenesis.
Therapeutic Relief for Erythrodermic Atopic Dermatitis
Authors: Dawn Z. Eichenfield
Journal: JAMA Dermatology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Dermatology journal
Effect of Focal vs Extended Irreversible Electroporation for the Ablation of Localized Low- or Intermediate-Risk Prostate Cancer on Early Oncological Control
Authors: Kai Zhang, Jeremy Teoh, Pilar Laguna, Jose Dominguez-Escrig, Eric Barret, Juan Casanova Ramon-Borja, Gordon Muir, Julia Bohr, Theo M. de Reijke, Paula Pelechano Gómez, Chi-Fai Ng, Rafael Sanchez-Salas, Jean de la Rosette
Journal: JAMA Surgery (2023)

Focal ablative irreversible electroporation (IRE) is a therapy that treats only the area of the tumor with the aim of achieving oncological control while reducing treatment-related functional detriment.
68Ga–DOTA–Exendin-4 PET/CT Demonstrated a Higher Detection Efficacy for Double-Primary Insulinomas Than MRI
Authors: Lin Qiu, Lianjun Lan, Liang Cai, Lin Chen, Yue Chen
Journal: Clinical Nuclear Medicine (2023)

We presented a 20-year-old woman with gradually increasing lethargy and multiple episodes of dizziness for 5 months. The laboratory examination revealed decreasing level of blood glucose and elevated levels of fasting plasma insulin and C-peptide. The MRI identified a focal nodule in the tail of the pancreas. 68Ga-DOTA-exendin-4 PET/CT revealed 2 intense focal tracer uptakes in the tail of the pancreas, one of which corresponded to the lesion revealed on MRI. The immunohistochemical results of resected samples confirmed the diagnosis of double-primary insulinomas. 68Ga-DOTA-exendin-4 PET/CT demonstrated excellent localization and characterization for double-primary insulinomas in the tail of the pancreas.
Quantifying and Interpreting the Prediction Accuracy of Models for the Time of a Cardiovascular Event—Moving Beyond C Statistic
Authors: Xuan Wang, Brian Lee Claggett, Lu Tian, Marcus Vinícius Bolívar Malachias, Marc A. Pfeffer, Lee-Jen Wei
Journal: JAMA Cardiology (2023)

Importance For personalized or stratified medicine, it is critical to establish a reliable and efficient prediction model for a clinical outcome of interest. The goal is to develop a parsimonious model with fewer predictors for broad future application without compromising predictability. A general approach is to construct various empirical models via individual patients’ specific baseline characteristics/biomarkers and then evaluate their relative merits. When the outcome of interest is the timing of a cardiovascular event, a commonly used metric to assess the adequacy of the fitted models is based on C statistics. These measures quantify a model’s ability to separate those who develop events earlier from those who develop them later or not at all (discrimination), but they do not measure how closely model estimates match observed outcomes (prediction accuracy). Metrics that provide clinically interpretable measures to quantify prediction accuracy are needed. Observations C statistics measure the concordance between the risk scores derived from the model and the observed event time observations. However, C statistics do not quantify the model prediction accuracy. The integrated Brier Score, which calculates the mean squared distance between the empirical cumulative event-free curve and its individual patient’s counterparts, estimates the prediction accuracy, but it is not clinically intuitive. A simple alternative measure is the average distance between the observed and predicted event times over the entire study population. This metric directly quantifies the model prediction accuracy and has often been used to evaluate the goodness of fit of the assumed models in settings other than survival data. This time-scale measure is easier to interpret than the C statistics or the Brier score. Conclusions and Relevance This article enhances our understanding of the model selection/evaluation process with respect to prediction accuracy. A simple, intuitive measure for quantifying such accuracy beyond C statistics can improve the reliability and efficiency of the selected model for personalized and stratified medicine.